You can override the BpmnPaletteProvider class, call the super method and remove a specific entry from the palette containers. Obviously you can also override the BpmnPaletteFactory and have it your way.

public void contributeToPalette(IEditorPart editor, Object content,
PaletteRoot root, Map predefinedEntries) {
//this is the short way
super.contributeToPalette(editor, content, root, predefinedEntries);
((PaletteContainer) root.getChildren().get(1)).getChildren().remove(0);
//the long way consists in populating the palette with your own factory.
}